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The Human Cell Atlas is a project to describe all cell types in the human body. The initiative was announced by a consortium after its inaugural meeting in London in October 2016, which established the first phase of the project. [1] [2] Aviv Regev and Sarah Teichmann defined the goals of the project at that meeting, [3] which was convened by the Broad Institute, the Wellcome Trust Sanger Institute and Wellcome Trust. [4] Regev and Teichmann lead the project. [5]
The Human Cell Atlas will catalogue a cell based on several criteria, specifically the cell type, its state, its location in the body, the transitions it undergoes, and its lineage. [6] It will gather data from existing research, and integrate it with data collected in future research projects. [2] Among the data it will collect is the fluxome, genome, metabolome, proteome, and transcriptome. [2]
Its scope is to categorize the 37 trillion cells of the human body to determine which genes each cell expresses by sampling cells from all parts of the body. [7]
All aspects of the project will be made "available to the public for free", including software and results. [8]
By April 2018, the project included more than 480 researchers conducting 185 projects. [9]
In October 2017, the Chan Zuckerberg Initiative announced funding for 38 projects related to the Human Cell Atlas. [10] Among them was a grant of undisclosed value to the Zuckerman Institute of the Columbia University Medical Center at Columbia University. [8] The grant, titled "A strategy for mapping the human spinal cord with single cell resolution", will fund research to identify and catalogue gene activity in all spinal cord cells. [8] The Translational Genomics Research Institute received a grant to develop a standard for the "processing and storage of solid tissues for single-cell RNA sequencing", compared to the typical practice of relying on the average of sequencing multiple cells. [10] Project home pages are available at the Chan Zuckerberg Initiative's website. [11]
The program is also backed by European Union, the National Institutes of Health in the United States, and the Manton Foundation. [7]
In April 2018, the first data set from the project was released, representing 530,000 immune system cells collected from bone marrow and cord blood. [9]
A research program at the Max Planck Institute of Immunobiology and Epigenetics published an atlas of the cells of the liver, using single-cell RNA sequencing on 10,000 normal cells obtained from nine donors. [12]
The Tabula Sapiens data was published on a dedicated website [13]
A cell type is a classification used to identify cells that share morphological or phenotypical features. A multicellular organism may contain cells of a number of widely differing and specialized cell types, such as muscle cells and skin cells, that differ both in appearance and function yet have identical genomic sequences. Cells may have the same genotype, but belong to different cell types due to the differential regulation of the genes they contain. Classification of a specific cell type is often done through the use of microscopy. Recent developments in single cell RNA sequencing facilitated classification of cell types based on shared gene expression patterns. This has led to the discovery of many new cell types in e.g. mouse cortex, hippocampus, dorsal root ganglion and spinal cord.
The Wellcome Sanger Institute, previously known as The Sanger Centre and Wellcome Trust Sanger Institute, is a non-profit British genomics and genetics research institute, primarily funded by the Wellcome Trust.
The Human Genome Project (HGP) was an international scientific research project with the goal of determining the base pairs that make up human DNA, and of identifying, mapping and sequencing all of the genes of the human genome from both a physical and a functional standpoint. It started in 1990 and was completed in 2003. It remains the world's largest collaborative biological project. Planning for the project started after it was adopted in 1984 by the US government, and it officially launched in 1990. It was declared complete on April 14, 2003, and included about 92% of the genome. Level "complete genome" was achieved in May 2021, with a remaining only 0.3% bases covered by potential issues. The final gapless assembly was finished in January 2022.
The Cancer Genome Project is part of the cancer, aging, and somatic mutation research based at the Wellcome Trust Sanger Institute in the United Kingdom. It aims to identify sequence variants/mutations critical in the development of human cancers. Like The Cancer Genome Atlas project within the United States, the Cancer Genome Project represents an effort in the War on Cancer to improve cancer diagnosis, treatment, and prevention through a better understanding of the molecular basis of the disease. The Cancer Genome Project was launched by Michael Stratton in 2000, and Peter Campbell is now the group leader of the project. The project works to combine knowledge of the human genome sequence with high throughput mutation detection techniques.
The Cancer Genome Atlas (TCGA) is a project to catalogue the genetic mutations responsible for cancer using genome sequencing and bioinformatics. The overarching goal was to apply high-throughput genome analysis techniques to improve the ability to diagnose, treat, and prevent cancer through a better understanding of the genetic basis of the disease.
Tyrosine-protein kinase, or Bromodomain adjacent to zinc finger domain, 1B (BAZ1B) is an enzyme that in humans is encoded by the BAZ1B gene.
Dual specificity protein phosphatase 3 is an enzyme that in humans is encoded by the DUSP3 gene.
Nuclear-interacting partner of ALK (NIPA), also known as zinc finger C3HC-type protein 1 (ZC3HC1), is a protein that in humans is encoded by the ZC3HC1 gene on chromosome 7. It is ubiquitously expressed in many tissues and cell types though exclusively expressed in the nuclear subcellular location. NIPA is a skp1 cullin F-box (SCF)-type ubiquitin E3 ligase (SCFNIPA) complex protein involved in regulating entry into mitosis. The ZC3HC1 gene also contains one of 27 SNPs associated with increased risk of coronary artery disease.
AT rich interactive domain 4A (RBP1-like), also known as ARID4A, is a protein which in humans is encoded by the ARID4A gene.
Kaptin is a protein that in humans is encoded by the KPTN gene.
Spermine synthase is an enzyme that in humans is encoded by the SMS gene. The protein encoded by this gene belongs to the spermidine/spermine synthases family. This gene encodes a ubiquitous enzyme of polyamine metabolism.
General transcription factor 3C polypeptide 5 is a protein that in humans is encoded by the GTF3C5 gene.
Putative Polycomb group protein ASXL1 is a protein that in humans is encoded by the ASXL1 gene.
N-terminal EF-hand calcium-binding protein 2 is a protein that in humans is encoded by the NECAB2 gene.
SLX4 is a protein involved in DNA repair, where it has important roles in the final steps of homologous recombination. Mutations in the gene are associated with the disease Fanconi anemia.
Aviv Regev is a computational biologist and systems biologist and Executive Vice President and Head of Genentech Research and Early Development in Genentech/Roche. She is a core member at the Broad Institute of MIT and Harvard and professor at the Department of Biology of the Massachusetts Institute of Technology. Regev is a pioneer of single cell genomics and of computational and systems biology of gene regulatory circuits. She founded and leads the Human Cell Atlas project, together with Sarah Teichmann.
Putative sodium-coupled neutral amino acid transporter 10, also known as solute carrier family 38 member 10, is a protein that in humans is encoded by the SLC38A10 gene.
Sarah Amalia Teichmann is a German scientist who is head of cellular genetics at the Wellcome Sanger Institute and a visiting research group leader at the European Bioinformatics Institute (EMBL-EBI). She serves as director of research in the Cavendish Laboratory, at the University of Cambridge and a senior research fellow at Churchill College, Cambridge.
The Earth BioGenome Project (EBP) is an initiative that aims to sequence and catalog the genomes of all of Earth's currently described eukaryotic species over a period of ten years. The initiative would produce an open DNA database of biological information that provides a platform for scientific research and supports environmental and conservation initiatives. A scientific paper presenting the vision for the project was published in PNAS in April 2018, and the project officially launched November 1, 2018.
Muzlifah Haniffa is a Malaysian dermatologist and immunologist who focuses on the development of the immune system and the use of single-cell techniques to understand biology. Haniffa is a professor and Wellcome Trust Senior Research Fellow in the Faculty of Medical Sciences at Newcastle University.